Author's Note

In short, this story is based on an alternative universe in which Nightmare Moon banished Celestia and became a despotic ruler. Some aliens helped her achieve this at the cost of the whole world being enslaved, with Nightmare Moon serving merely as a puppet dictator.

This was one shot at how the ending of all that might have went. Since you don't mess around with aliens who travel between dimensions, the apparent victory of an ensemble cast and return of good ol' Celly wasn't enough to drive them back. The idea of the Reaper-esque dialogue (Mass Effect trilogy) was dropped due to already being a crossover with one series and so was the inclusion of the Doctor from Doctor Who.

Legends speak of wizards who would be able to swiftly use all those ideas and make them work, but I am not a wizard. Plus, it would cross over with waaaayyy too many things at once.

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"Your world exists because we allow it and will end because we demand it." said an eerie voice and the message appeared in written form on all screens. It stayed there for a few seconds before showings spaceships around Equus and then turned off.

"I... I don't understand." said Twilight. "We fullfilled the prophecy, we brough you back and drove them away from Equestria, was that not enough?"

"I'm afraid it wasn't, Twilight." said Celestia. "Not even I can battle with such a force and fleet, but there is one thing I can do."

"The thing being?" asked Trixie.

"I can transmit an universe-wide calling for help but I can't guarrantee someone will come to save us." she answered. "With Luna gone, It's the only thing I can do."

"Well... what's keeping you?" asked Twilight. Celestia nodded, approached one of the terminals and then begun speaking.

"We have fullfilled the prophecy, drove them out of planet and lost countless lives to our cause. But that wasn't enough. If anyone out there is willing to help us, please do so. You are our only chance." After transmitting said message, they waited but didn't get a reply. Before they would accept their fate, however, they heard a wheezing and an unknown object started to materialise in the center of the room. As the sound became louder, the object also started to become clearer. It was partially transparent at first, but moments later, the sounds stopped and it was there, a big blue box with many small windows and a single door. Twilight and the rest of the gang could barely believe their own eyes.

Suddenly, the doors opened and a clothed, bipedal creature walked out of it. By the looks of his face, he was equally suprised to seem them as they were.

"Ponies?" he said. "That's... weird." He took something from his pocket and aimed it at them. It was the size of a small stick and produced a high-pitched sound when he aimed it at Twilight. He did this with the rest of the ponies in the room and then tucked it back into his pocket. The ponies looked at each other, puzzled and confused by his actions.

"Now, who of you was calling for a Doctor?" he asked.